The experiment of high temperature on the two different types of Bt cotton cultivars was conducted at different developing periods, the results showed that the high temperature at 37℃ for 48 hours had less effect on the leaf Bt protein content in the peak squaring period and the blooming period; however, the Bt protein content decreased significantly in the peak boll period, and that of Kemian No.1 decreased significantly after being treated within 36 hours, while that of Xinyang 822 dropped sharply after 36 hours. Further more, the key enzyme activity of the nitrogen metabolism showed that the leaf protease and peptidase activity increased, the leaf GPT activity decreased but the content of amino acid increased during high temperature treatment of 37℃ for 48 hours at peak boll period.